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Question: gene set (enrichment) analysis
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gravatar for Bogdan
2.1 years ago by
Bogdan480
Palo Alto, CA, USA
Bogdan480 wrote:

Dear all,

 

please could you advise about the best BioC/R package to use for gene set enrichment analysis ;)

on a side note, may I ask the same question about the easiest package to use for survival analysis :)

many thanks,

-- bogdan

 

 

ADD COMMENTlink modified 2.1 years ago by Axel Klenk830 • written 2.1 years ago by Bogdan480

have you tried the gsea package from the broad institute?

or the gage package 

ADD REPLYlink written 2.1 years ago by Assa Yeroslaviz1.4k
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gravatar for b.nota
2.1 years ago by
b.nota290
Netherlands
b.nota290 wrote:

I recommend the GOseq package for GO enrichment analysis, it's quite easy in use if you read the manual first. You only need a list of your significant genes and a list of all your assayed genes.

ADD COMMENTlink written 2.1 years ago by b.nota290
0
gravatar for Bogdan
2.1 years ago by
Bogdan480
Palo Alto, CA, USA
Bogdan480 wrote:

thank you !

ADD COMMENTlink written 2.1 years ago by Bogdan480
0
gravatar for Axel Klenk
2.1 years ago by
Axel Klenk830
Switzerland
Axel Klenk830 wrote:

Dear Bogdan,

I'm a bit late for your question but I think the limma package must be mentioned: see the help pages for camera, roast and romer. These are gene set tests, not enrichment tests, i.e., no DEG list required.

Cheers,

 - axel

 

ADD COMMENTlink written 2.1 years ago by Axel Klenk830

thanks Axel !

ADD REPLYlink written 2.1 years ago by Bogdan480
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